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- PDB-8x0i: X-Ray crystal structure of glycoside hydrolase family 6 cellobioh... -

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Basic information

Entry
Database: PDB / ID: 8x0i
TitleX-Ray crystal structure of glycoside hydrolase family 6 cellobiohydrolase from Phanerochaete chrysosporium PcCel6A C240S/C393S soaked in cellobioimidazole
ComponentsGlucanase
KeywordsHYDROLASE / Glycoside hydrolase family 6 / cellobiohydrolase / cellulase / catalytic domain / mutant
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain
Similarity search - Domain/homology
Chem-IDC / Glucanase
Similarity search - Component
Biological speciesPhanerodontia chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsYamaguchi, S. / Sunagawa, N. / Tachioka, M. / Igarashi, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22J12651 Japan
CitationJournal: To Be Published
Title: Activity and X-ray crystal structure of candidate base catalyst mutants of glycoside hydrolase family 6 cellobiohydrolase
Authors: Yamaguchi, S. / Sunagawa, N. / Tachioka, M. / Igarashi, K.
History
DepositionNov 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7122
Polymers38,3491
Non-polymers3621
Water10,953608
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Software (PISA) determined protein interfaces have not revealed any specific interactions that could form stable quaternary structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.825, 67.239, 88.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucanase


Mass: 38349.445 Da / Num. of mol.: 1 / Mutation: C240S, C393S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerodontia chrysosporium (fungus) / Strain: K-3 / Gene: cel6A / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: H3K419, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Sugar ChemComp-IDC / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside / 5-HYDROXYMETHYL-5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDIN-6YL-7,8-DIOL-GLUCOPYRANOSIDE / IMIDAZOLE-DERIVED CELLOBIOSE / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl D-glucoside / (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl glucoside


Type: D-saccharide / Mass: 362.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: PEG 4000, sodium acetate, sodium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→46.59 Å / Num. obs: 137125 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 7.03 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.8
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4782 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→38.29 Å / SU ML: 0.0636 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.4262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1493 6844 4.99 %
Rwork0.1359 130186 -
obs0.1365 137031 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.77 Å2
Refinement stepCycle: LAST / Resolution: 1.08→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 25 608 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523795
X-RAY DIFFRACTIONf_angle_d0.88865262
X-RAY DIFFRACTIONf_chiral_restr0.0793574
X-RAY DIFFRACTIONf_plane_restr0.0075724
X-RAY DIFFRACTIONf_dihedral_angle_d5.8655543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.21011260.20792801X-RAY DIFFRACTION62.85
1.09-1.110.18721890.18063727X-RAY DIFFRACTION85.11
1.11-1.120.17972070.16844067X-RAY DIFFRACTION91.7
1.12-1.130.18012300.15594218X-RAY DIFFRACTION96.46
1.13-1.150.18562310.14994278X-RAY DIFFRACTION97.56
1.15-1.160.15552140.1424330X-RAY DIFFRACTION98.59
1.16-1.180.14112340.14024383X-RAY DIFFRACTION99.33
1.18-1.20.15442590.13764331X-RAY DIFFRACTION100
1.2-1.220.15172290.13854441X-RAY DIFFRACTION100
1.22-1.240.14442430.14094396X-RAY DIFFRACTION100
1.24-1.260.15172530.13444352X-RAY DIFFRACTION99.98
1.26-1.280.14912230.14044434X-RAY DIFFRACTION100
1.28-1.310.15282200.13714426X-RAY DIFFRACTION100
1.31-1.330.1522600.13764376X-RAY DIFFRACTION100
1.33-1.360.15872420.13734408X-RAY DIFFRACTION100
1.36-1.390.15192480.13714388X-RAY DIFFRACTION100
1.39-1.430.14772450.1374405X-RAY DIFFRACTION100
1.43-1.470.1372250.13184446X-RAY DIFFRACTION99.98
1.47-1.510.14212420.1274403X-RAY DIFFRACTION100
1.51-1.560.13532190.12644455X-RAY DIFFRACTION100
1.56-1.610.13522310.12174436X-RAY DIFFRACTION100
1.61-1.680.14192580.12664423X-RAY DIFFRACTION100
1.68-1.750.14152490.1294425X-RAY DIFFRACTION100
1.75-1.850.15692120.13574489X-RAY DIFFRACTION100
1.85-1.960.15542320.13684475X-RAY DIFFRACTION100
1.96-2.110.12342230.12964491X-RAY DIFFRACTION100
2.11-2.330.1572260.12954494X-RAY DIFFRACTION100
2.33-2.660.15892250.14274530X-RAY DIFFRACTION100
2.66-3.360.15052110.13834599X-RAY DIFFRACTION100
3.36-36.920.13832380.12684759X-RAY DIFFRACTION100

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